Zinc in PDB 8tlh: CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo

The structure of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo, PDB code: 8tlh was solved by J.R.Horton, R.Ren, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.71 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.679, 31.523, 91.634, 90, 110.59, 90
R / Rfree (%)	19.9 / 22.7

The structure of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo (pdb code 8tlh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo, PDB code: 8tlh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:34.1 occ:1.00 SG A:CYS284 2.3 35.9 1.0 SG A:CYS281 2.3 29.9 1.0 SG A:CYS308 2.3 34.9 1.0 SG A:CYS311 2.4 33.1 1.0 CB A:CYS311 3.0 31.1 1.0 CB A:CYS281 3.1 22.2 1.0 CB A:CYS284 3.2 37.0 1.0 N A:CYS284 3.6 36.0 1.0 NZ A:LYS271 3.6 35.6 1.0 CB A:CYS308 3.6 36.6 1.0 CA A:CYS284 4.0 33.1 1.0 N A:CYS308 4.1 29.7 1.0 CA A:CYS311 4.3 37.2 1.0 CB A:GLN283 4.3 26.7 1.0 CA A:CYS308 4.5 32.8 1.0 N A:CYS311 4.5 46.1 1.0 CA A:CYS281 4.6 30.6 1.0 O A:HOH507 4.6 28.4 1.0 C A:GLN283 4.6 40.0 1.0 CA A:GLN283 4.9 34.4 1.0 N A:GLN283 4.9 36.6 1.0 C A:CYS284 4.9 34.4 1.0 CE A:LYS271 4.9 37.3 1.0 C A:CYS281 5.0 31.9 1.0

Zinc binding site 2 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:35.1 occ:1.00 NE2 A:HIS282 2.0 29.4 1.0 SG A:CYS343 2.3 41.9 1.0 SG A:CYS338 2.3 35.1 1.0 SG A:CYS340 2.3 32.9 1.0 CD2 A:HIS282 2.9 31.1 1.0 CB A:CYS343 3.0 33.6 1.0 CE1 A:HIS282 3.1 35.0 1.0 CB A:CYS338 3.4 38.8 1.0 CB A:CYS340 3.4 29.7 1.0 CG A:HIS282 4.1 34.4 1.0 ND1 A:HIS282 4.1 30.2 1.0 N A:CYS343 4.1 32.5 1.0 CA A:CYS343 4.2 45.0 1.0 N A:CYS340 4.2 37.6 1.0 CA A:CYS340 4.4 30.6 1.0 CG A:PRO333 4.5 32.0 1.0 O A:HOH517 4.5 32.6 1.0 C2 A:EDO401 4.6 57.0 1.0 O A:HOH543 4.6 51.6 1.0 CA A:CYS338 4.7 32.1 1.0 C A:CYS338 4.8 37.6 1.0 C A:CYS340 5.0 35.1 1.0

Zinc binding site 3 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:38.1 occ:1.00 SG A:CYS300 2.2 36.6 1.0 SG A:CYS295 2.3 36.1 1.0 SG A:CYS331 2.3 37.2 1.0 SG A:CYS334 2.3 40.8 1.0 CB A:CYS300 3.0 34.3 1.0 CB A:CYS295 3.2 38.8 1.0 CB A:CYS334 3.4 38.0 1.0 CB A:CYS331 3.5 29.9 1.0 NH1 A:ARG304 3.8 41.3 1.0 N A:CYS331 3.8 30.2 1.0 CA A:CYS300 4.2 38.2 1.0 CA A:CYS331 4.2 33.4 1.0 N A:CYS334 4.3 34.4 1.0 CA A:CYS334 4.4 36.8 1.0 CB A:ASN297 4.5 40.2 1.0 CA A:GLY305 4.6 34.3 1.0 CA A:CYS295 4.7 43.2 1.0 CG A:ARG304 4.7 34.8 1.0 O A:CYS331 4.8 38.5 1.0 O A:HOH519 4.9 37.9 1.0 C A:CYS331 4.9 35.3 1.0 ND2 A:ASN297 4.9 47.7 1.0 CZ A:ARG304 4.9 38.1 1.0 N A:GLY305 4.9 34.0 1.0 C A:HIS330 5.0 41.3 1.0

Zinc binding site 4 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:46.8 occ:1.00 SG B:CYS308 2.3 45.5 1.0 SG B:CYS284 2.3 44.7 1.0 SG B:CYS311 2.3 48.3 1.0 SG B:CYS281 2.4 48.5 1.0 CB B:CYS311 3.0 56.1 1.0 CB B:CYS281 3.2 41.0 1.0 CB B:CYS284 3.2 52.6 1.0 N B:CYS284 3.5 43.1 1.0 NZ B:LYS271 3.6 48.8 1.0 CB B:CYS308 3.6 51.5 1.0 CA B:CYS284 4.0 39.9 1.0 N B:CYS308 4.1 47.8 1.0 CA B:CYS311 4.3 51.7 1.0 CB B:GLN283 4.3 40.3 1.0 N B:CYS311 4.4 55.2 1.0 CA B:CYS308 4.4 51.5 1.0 C B:GLN283 4.6 46.8 1.0 CA B:CYS281 4.6 43.9 1.0 O B:HOH502 4.6 45.1 1.0 CA B:GLN283 4.8 45.4 1.0 N B:GLN283 4.8 44.0 1.0 C B:CYS284 4.9 47.4 1.0 CE B:LYS271 4.9 44.4 1.0 C B:CYS281 5.0 53.8 1.0

Zinc binding site 5 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:50.0 occ:1.00 NE2 B:HIS282 2.0 43.2 1.0 SG B:CYS343 2.2 57.5 1.0 SG B:CYS338 2.3 51.7 1.0 SG B:CYS340 2.3 47.2 1.0 CD2 B:HIS282 2.9 47.2 1.0 CE1 B:HIS282 3.0 54.8 1.0 CB B:CYS343 3.0 49.7 1.0 CB B:CYS340 3.4 53.4 1.0 CB B:CYS338 3.5 59.4 1.0 CG B:HIS282 4.0 48.5 1.0 ND1 B:HIS282 4.1 48.9 1.0 N B:CYS343 4.2 54.4 1.0 CA B:CYS343 4.2 56.2 1.0 N B:CYS340 4.3 52.2 1.0 CA B:CYS340 4.4 49.3 1.0 CG B:PRO333 4.6 51.6 1.0 CA B:CYS338 4.7 52.2 1.0 C B:CYS338 4.8 57.7 1.0 C B:CYS340 5.0 54.1 1.0 O B:HIS282 5.0 47.4 1.0

Zinc binding site 6 out of 6 in the CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of CDCA7 (Mouse) Binds Non-B-Form 32-Mer Dna Oligo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:59.2 occ:1.00 SG B:CYS334 2.2 60.7 1.0 SG B:CYS331 2.3 56.1 1.0 SG B:CYS295 2.3 55.9 1.0 SG B:CYS300 2.4 55.4 1.0 CB B:CYS300 3.0 64.3 1.0 CB B:CYS295 3.3 60.2 1.0 CB B:CYS334 3.3 57.5 1.0 CB B:CYS331 3.4 49.1 1.0 N B:CYS331 3.8 56.0 1.0 NH1 B:ARG304 3.9 68.8 1.0 CA B:CYS331 4.2 53.2 1.0 N B:CYS334 4.2 64.0 1.0 CA B:CYS300 4.2 65.0 1.0 CA B:CYS334 4.3 58.8 1.0 CA B:GLY305 4.6 61.3 1.0 CB B:ASN297 4.6 65.6 1.0 CG B:ARG304 4.7 64.4 1.0 CA B:CYS295 4.7 58.3 1.0 O B:CYS331 4.7 58.0 1.0 C B:CYS331 4.8 53.7 1.0 O B:HOH504 4.9 54.2 1.0 CZ B:ARG304 4.9 66.0 1.0 N B:GLY305 4.9 56.5 1.0 C B:HIS330 5.0 64.7 1.0 ND2 B:ASN297 5.0 70.5 1.0

S.Hardikar, R.Ren, Z.Ying, J.R.Horton, M.D.Bramble, B.Liu, Y.Lu, J.Dan, X.Zhang, X.Cheng, T.Chen. The Icf Syndrome Protein CDCA7 Harbors A Unique Dna-Binding Domain That Recognizes A Cpg Dyad in the Context of A Non-B Dna Sci Adv 2024.
ISSN: ESSN 2375-2548